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- PDB-3fn2: Crystal structure of a putative sensor histidine kinase domain fr... -

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Basic information

Entry
Database: PDB / ID: 3fn2
TitleCrystal structure of a putative sensor histidine kinase domain from Clostridium symbiosum ATCC 14940
ComponentsPutative sensor histidine kinase domain
KeywordsTRANSFERASE / gut microbiome / sensor histidine kinase / Structural Genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyhistidine kinase doma clostridium symbiosum atcc 14940 / histidine kinase doma clostridium symbiosum atcc 14940 / 2-Layer Sandwich / Alpha Beta / : / PHOSPHATE ION
Function and homology information
Biological speciesClostridium symbiosum ATCC 14940 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsCuff, M.E. / Tesar, C. / Freeman, L. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: TO BE PUBLISHED
Title: The structure of a putative sensor histidine kinase domain from Clostridium symbiosum ATCC 14940
Authors: Cuff, M.E. / Tesar, C. / Freeman, L. / Joachimiak, A.
History
DepositionDec 23, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative sensor histidine kinase domain
B: Putative sensor histidine kinase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,6155
Polymers25,4192
Non-polymers1963
Water2,774154
1
A: Putative sensor histidine kinase domain
B: Putative sensor histidine kinase domain
hetero molecules

A: Putative sensor histidine kinase domain
B: Putative sensor histidine kinase domain
hetero molecules

A: Putative sensor histidine kinase domain
B: Putative sensor histidine kinase domain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,84615
Polymers76,2586
Non-polymers5889
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area22860 Å2
ΔGint-151.2 kcal/mol
Surface area25860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.252, 107.252, 49.710
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number146
Space group name H-MH3
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

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Components

#1: Protein Putative sensor histidine kinase domain


Mass: 12709.665 Da / Num. of mol.: 2 / Fragment: Residues 41-143
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium symbiosum ATCC 14940 (bacteria)
Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 43.18 %
Crystal growTemperature: 296 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 0.1M Acetate pH 4.5, 0.8M NaH2PO4, 1.4M K2HPO3, VAPOR DIFFUSION, SITTING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.97945, 0.97921
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Oct 9, 2008
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979451
20.979211
ReflectionRedundancy: 5.6 % / Av σ(I) over netI: 30.42 / Number: 91098 / Rmerge(I) obs: 0.091 / Χ2: 2.37 / D res high: 1.9 Å / D res low: 50 Å / Num. obs: 16144 / % possible obs: 95.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.165096.310.0912.5996.1
4.095.1695.410.0695.9235
3.584.0999.810.0674.5095.6
3.253.5899.910.0723.5335.8
3.023.2510010.0822.7035.9
2.843.0299.910.0922.0355.9
2.72.8499.910.111.795.9
2.582.710010.1191.5596.1
2.482.5810010.1161.3126
2.392.4810010.1381.2386
2.322.3910010.161.1266.1
2.252.3210010.1781.0326
2.192.2510010.1850.9055.9
2.142.1910010.2120.8915.7
2.092.1498.810.2220.8185.4
2.052.0996.310.2580.8125.1
2.012.0590.710.2880.7955.1
1.972.0184.210.3270.7335.2
1.931.9779.510.3920.7664.9
1.91.9373.610.4860.7114.5
ReflectionResolution: 1.9→50 Å / Num. all: 16144 / Num. obs: 16144 / % possible obs: 95.7 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Rmerge(I) obs: 0.091 / Χ2: 2.37 / Net I/σ(I): 30.418
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.486 / Num. unique all: 626 / Χ2: 0.711 / % possible all: 73.6

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Phasing

PhasingMethod: MAD
Phasing MADD res high: 1.9 Å / D res low: 50 Å / FOM : 0 / FOM acentric: 0.35 / FOM centric: 0 / Reflection: 0 / Reflection acentric: 16072 / Reflection centric: 0
Phasing MAD set

R cullis centric: 0 / Highest resolution: 1.9 Å / Lowest resolution: 50 Å / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDR cullis acentricLoc acentricPower acentricReflection acentric
11.610.3016072
20.911.30.6614164
Phasing MAD set shell

R cullis centric: 0 / Loc centric: 0 / Power centric: 0 / Reflection centric: _

IDResolution (Å)R cullis acentricLoc acentricPower acentricReflection acentric
112.01-501.661.6053
16.82-12.011.431.40284
14.76-6.821.4110669
13.66-4.761.040.601275
12.97-3.661.360.302050
12.5-2.973.020.202962
12.16-2.55.920.104059
11.9-2.161.960.104720
212.01-500.7419.21.9351
26.82-12.010.7819.61.62280
24.76-6.820.7416.31.61668
23.66-4.760.8317.30.981272
22.97-3.660.8712.60.822049
22.5-2.970.939.50.592957
22.16-2.50.979.40.334058
21.9-2.160.999.90.22829
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se56.90908-0.444-0.821-0.0950
2Se40.21751-0.455-0.8130.0520
3Se27.10509-0.579-0.833-0.0380
4Se37.5885-0.404-0.910.0030
5Se73.88927-0.303-0.836-0.10
6Se43.29974-0.263-0.8060.0540
7Se60.29614-0.444-0.821-0.096-0.148
8Se43.25515-0.455-0.8130.051-0.15
9Se30.8031-0.579-0.834-0.039-0.115
10Se36.22847-0.404-0.910.002-0.087
11Se77.62359-0.303-0.836-0.101-0.1
12Se51.3333-0.262-0.8060.054-0.101
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflection acentricReflection centricReflection
12.01-5000.6880530
6.82-12.0100.71802840-1073754472
4.76-6.8200.74306690
3.66-4.7600.641012750
2.97-3.6600.596020500135909581
2.5-2.9700.4290296203
2.16-2.500.258040590-1
1.9-2.1600.114047200
Phasing dmMethod: Solvent flattening and histogram matching / Reflection: 16072
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
6.01-10047.10.84508
4.75-6.0143.30.921516
4.15-4.75460.937513
3.79-4.1544.80.915512
3.53-3.7942.70.917518
3.32-3.5347.50.905505
3.16-3.3246.50.901515
3.02-3.1644.70.886532
2.9-3.0252.40.86532
2.79-2.948.90.867574
2.69-2.7954.20.828600
2.61-2.6956.70.84610
2.53-2.6156.50.84622
2.45-2.5358.80.844655
2.39-2.4559.50.821674
2.33-2.3960.60.804699
2.27-2.3362.60.8698
2.22-2.2768.90.812731
2.17-2.2269.30.834764
2.12-2.1772.10.818747
2.08-2.1273.70.821759
2.03-2.0877.40.847780
2-2.0375.50.828716
1.96-276.90.779664
1.9-1.96790.7471128

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MLPHAREphasing
DM6phasing
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
SHELXDphasing
SHELXEmodel building
SOLVEphasing
RESOLVEphasing
ARP/wARPmodel building
CCP4phasing
Omodel building
Cootmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.9→50 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.936 / Occupancy max: 1 / Occupancy min: 0.33 / SU B: 8.653 / SU ML: 0.118 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.17
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 812 5.1 %RANDOM
Rwork0.187 ---
all0.19 16072 --
obs0.19 16072 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 139.7 Å2 / Biso mean: 33.198 Å2 / Biso min: 13.3 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å2-1.21 Å20 Å2
2---2.41 Å20 Å2
3---3.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1622 0 10 154 1786
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221700
X-RAY DIFFRACTIONr_bond_other_d0.0010.021190
X-RAY DIFFRACTIONr_angle_refined_deg1.4751.9732283
X-RAY DIFFRACTIONr_angle_other_deg0.85132887
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.045202
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.3124.62493
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.33815334
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.0621512
X-RAY DIFFRACTIONr_chiral_restr0.0830.2237
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021891
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02363
X-RAY DIFFRACTIONr_mcbond_it0.9251.5981
X-RAY DIFFRACTIONr_mcbond_other0.2391.5409
X-RAY DIFFRACTIONr_mcangle_it1.68721581
X-RAY DIFFRACTIONr_scbond_it2.7463719
X-RAY DIFFRACTIONr_scangle_it4.3984.5701
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 53 -
Rwork0.245 883 -
all-936 -
obs--75.36 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.1249-0.27360.34582.53770.73822.1390.01660.0260.22740.0397-0.0619-0.2561-0.1282-0.02990.04520.0148-0.0059-0.00470.0370.01140.060616.32886.75233.5816
22.2041-0.48230.07072.84560.6651.65850.06680.1328-0.0296-0.1106-0.0448-0.28970.0661-0.0284-0.0220.0126-0.00560.01510.05270.00170.060717.61720.775430.7089
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A43 - 139
2X-RAY DIFFRACTION2B43 - 139

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